On all the cameras I have there actually is an IQ compromise when shooting at base ISO. For example on my D800 there is more noise and shadow tinting when using ISO 100 pushed to ISO 3200/6400 than when shooting at ISO 800 and pushed to the same output brightness.

Interesting. According to sensorgen's figures (derived from DxOMark data), that should not be the case. That said, I've heard that some (most?) RAW converters may make use of the ISO setting information in the conversion. For example, an ISO 100 file will be converted differently than an ISO 800 file, based on assumptions about the scene as a function of the selected ISO. Perhaps someone can confirm or deny this.

Yeah, in my testing both the quantity and quality of noise is worse for a 100->3200 vs an 800->3200. That's not to say 100->3200 is horrible but for certain scenes I've found a definitive disadvantage to using 100. The worst is the shadow tinting/hue shifts, which on the D800 aren't so bad but are worse on the D600 and downright horrible on the D7100. The best camera/sensor in this regard is the 16MP Exmor in the D7000/D5100.

What raw converter are you using? and is the profile twisted?

I've noticed the same thing with my D800, using LR 4.x/ACR. I actually started trying it with several other cameras after I read Bob's posts about the subject a few years ago. I chalked it up to my not using the right raw converter, but then never followed up with trying to find the right one for demonstrating this.